Dry matter intake in US Holstein cows: Exploring the genomic and phenotypic impact of milk components and body weight composite

Large datasets allow estimation of feed required for individual milk components or body maintenance. Phenotypic regressions are useful for nutrition management, but genetic regressions are more useful in breeding programs. Dry matter intake records from 8,513 lactations of 6,621 Holstein cows were predicted from phenotypes or genomic evaluations for milk components and body size traits. The mixed models also included DIM, age-parity subclass, trial date, management group, and BW change during 28- and 42-d feeding trials in mid lactation. Phenotypic regressions of DMI on milk (0.014 ± 0.006), fat (3.06 ± 0.01), and protein (4.79 ± 0.25) were much less than corresponding genomic regressions (0.08 ± 0.03, 11.30 ± 0.47, and 9.35 ± 0.87, respectively) or sire genomic regressions multiplied by 2 (0.048 ± 0.04, 6.73 ± 0.94, and 4.98 ± 1.75). Thus, marginal feed costs as fractions of marginal milk revenue were higher from genetic than phenotypic regressions. According to the ECM formula, fat production requires 69% more DMI than protein production. In the phenotypic regression, it was estimated that protein production requires 56% more DMI than fat. However, the genomic regression for the animal showed a difference of only 21% more DMI for protein compared with fat, whereas the sire genomic regressions indicated approximately 35% more DMI for fat than protein. Estimates of annual maintenance in kilograms DMI/kilograms BW per lactation were similar from phenotypic regression (5.9 ± 0.14), genomic regression (5.8 ± 0.31), and sire genomic regression multiplied by 2 (5.3 ± 0.55) and are larger than those estimated by the National Academies for Science, Engineering, and Medicine based on NEL equations. Multiple regressions on genomic evaluations for the 5 type traits in body weight composite (BWC) showed that strength was the type trait most associated with BW and DMI, agreeing with the current BWC formula, whereas other traits were less useful predictors, especially for DMI. The Net Merit formula used to weight different genetic traits to achieve an economically optimal overall selection response was revised in 2021 to better account for these estimated regressions. To improve profitability, breeding programs should select smaller cows with negative residual feed intake that produce more milk, fat, and protein.

Epigenetic regulation of functional candidate genes for milk production traits in dairy sheep subjected to protein restriction in the prepubertal stage

BACKGROUND

As the prepubertal stage is a crucial point for the proper development of the mammary gland and milk production, this study aims to evaluate how protein restriction at this stage can affect methylation marks in milk somatic cells. Here, 28 Assaf ewes were subjected to 42.3% nutritional protein restriction (14 animals, NPR) or fed standard diets (14 animals, C) during the prepubertal stage. During the second lactation, the milk somatic cells of these ewes were sampled, and the extracted DNA was subjected to whole-genome bisulfite sequencing.

RESULTS

A total of 1154 differentially methylated regions (DMRs) were identified between the NPR and C groups. Indeed, the results of functional enrichment analyses of the genes harboring these DMRs suggested their relevant effects on the development of the mammary gland and lipid metabolism in sheep. The additional analysis of the correlations of the mean methylation levels within these DMRs with fat, protein, and dry extract percentages in the milk and milk somatic cell counts suggested associations between several DMRs and milk production traits. However, there were no phenotypic differences in these traits between the NPR and C groups.

CONCLUSION

In light of the above, the results obtained in the current study might suggest potential candidate genes for the regulation of milk production traits in the sheep mammary gland. Further studies focusing on elucidating the genetic mechanisms affected by the identified DMRs may help to better understand the biological mechanisms modified in the mammary gland of dairy sheep as a response to nutritional challenges and their potential effects on milk production.

Intergenerational impact of dietary protein restriction in dairy ewes on epigenetic marks in the perirenal fat of their suckling lambs

In sheep, nutrition during the prepubertal stage is essential for growth performance and mammary gland development. However, the potential effects of nutrient restriction in a prepuberal stage over the progeny still need to be better understood. Here, the intergenerational effect of maternal protein restriction at prepubertal age (2 months of age) on methylation patterns was evaluated in the perirenal fat of Assaf suckling lambs. In total, 17 lambs from ewes subjected to dietary protein restriction (NPR group, 44% less protein) and 17 lambs from control ewes (C group) were analyzed. These lambs were ranked based on their carcass proportion of perirenal and cavitary fat and classified into HighPCF and LowPCF groups. The perirenal tissue from 4 NPR-LowPCF, 4 NPR-HighPCF, 4 C-LowPCF, and 4 C-HighPCF lambs was subjected to whole-genome bisulfite sequencing and differentially methylated regions (DMRs) were identified. Among other relevant processes, these DMRs were mapped in genes responsible for regulating the transition of brown to white adipose tissue and nonshivering thermoregulation, which might be associated with better adaptation/survival of lambs in the perinatal stage. The current study provides important biological insights about the intergenerational effect on the methylation pattern of an NPR in replacement ewes.

Skeletal Muscle Expression of Actinin-3 (ACTN3) in Relation to Feed Efficiency Phenotype of F2Bos indicus - Bos taurus Steers

In this study, actinin-3 (ACTN3) gene expression was investigated in relation to the feed efficiency phenotype in Bos indicus - Bos taurus crossbred steers. A measure of relative feed efficiency based on residual feed intake relative to predictions from the NRC beef cattle model was analyzed by the use of a mixed linear model that included sire and family nested within sire as fixed effects and age, animal type, sex, condition, and breed as random effects for 173 F₂ Nellore-Angus steers. Based on these residual intake observations, individuals were ranked from most efficient to least efficient. Skeletal muscle samples were analyzed from 54 steers in three groups of 18 (high efficiency, low efficiency, and a statistically average group). ACTN3, which encodes a muscle-specific structural protein, was previously identified as a candidate gene from a microarray analysis of RNA extracted from muscle samples obtained from a subset of steers from each of these three efficiency groups. The expression of ACTN3 was evaluated by quantitative reverse transcriptase PCR analysis. The expression of ACTN3 in skeletal muscle was 1.6-fold greater in the inefficient steer group than in the efficient group (p = 0.007). In addition to expression measurements, blocks of SNP haplotypes were assessed for breed or parent of origin effects. A maternal effect was observed for ACTN3 inheritance, indicating that a maternal B. indicus block conferred improved residual feed efficiency relative to the B. taurus copy (p = 0.03). A SNP haplotype analysis was also conducted for m-calpain (CAPN2) and fibronectin 1 (FN1), and a significant breed effect was observed for both genes, with B. indicus and B. taurus alleles each conferring favorable efficiency when inherited maternally (p = 0.03 and p = 0.04). Because the ACTN3 structural protein is specific to fast-twitch (type II) muscle fibers and not present in slow-twitch muscle fibers (type I), muscle samples used for expression analysis were also assayed for fiber type ratio (type II/type I). Inefficient animals had a fast fiber type ratio 1.8-fold greater than the efficient animals (p = 0.027). Because these fiber-types exhibit different metabolic profiles, we hypothesize that animals with a greater proportion of fast-twitch muscle fibers are also less feed efficient.

Genetic mechanisms underlying feed utilization and implementation of genomic selection for improved feed efficiency in dairy cattle

The economic importance of genetically improving feed efficiency has been recognized by cattle producers worldwide. It has the potential to considerably reduce costs, minimize environmental impact, optimize land and resource use efficiency, and improve the overall cattle industry’s profitability. Feed efficiency is a genetically complex trait that can be described as units of product output (e.g., milk yield) per unit of feed input. The main objective of this review paper is to present an overview of the main genetic and physiological mechanisms underlying feed utilization in ruminants and the process towards implementation of genomic selection for feed efficiency in dairy cattle. In summary, feed efficiency can be improved via numerous metabolic pathways and biological mechanisms through genetic selection. Various studies have indicated that feed efficiency is heritable, and genomic selection can be successfully implemented in dairy cattle with a large enough training population. In this context, some organizations have worked collaboratively to do research and develop training populations for successful implementation of joint international genomic evaluations. The integration of “-omics” technologies, further investments in high-throughput phenotyping, and identification of novel indicator traits will also be paramount in maximizing the rates of genetic progress for feed efficiency in dairy cattle worldwide.

A whole-farm investment analysis of a partial mixed ration feeding system for dairy cows

Aim A dairy farm in south-west Victoria was analysed to discern the impact on profit and risk of changing from a feeding system in the base case where grain was fed in the dairy and forage in the paddock, to a partial mixed ration (PMR) or a formulated grain mix (FGM) feeding system. Context A PMR feeding system involves feeding a well formulated mixed ration to a grazing dairy herd and typically requires the use of specialised machinery to mix and feed out the forage and grain components of the ration together onto a feed pad. In a FGM feeding system, the same formulated ration fed in the PMR system is used, but the grain component of the ration is fed using the existing feeding system in the dairy with the hay component fed in the paddock. Method The analysis used data from experiments recently performed to establish milk responses to mixed ration feeding under Australian conditions. The case study farm comprised 244 ha and a herd of 420 self-replacing Holstein-Friesian cows that calved from May to July. The herd feeding system was based on grazed pasture, grain fed in the dairy at milking and hay fed in the paddock. Supplementary feed comprised ~50% of metabolisable energy in the diet of the milking cows. The pre-existing feeding system was altered to incorporate either a PMR system or a FGM system. An increased herd size of an extra 100 cows, plus the PMR or FGM systems, was also tested. Key results All systems analysed were more profitable than the base case. Increasing the herd by 100 cows was the most profitable option for both the PMR and FGM systems, but intensifying the system by increasing cow numbers also had the most variability in profit. Conclusions and implications The FGM system was the most profitable system because milk production could be increased without the costs of extra labour, depreciation and repairs and maintenance associated with using a mixer wagon to feed the ration. The FGM system presents an option for farmers to expand or intensify their systems without needing to construct a feed pad or invest in extra machinery and equipment.

The assessment of supplementation requirements of grazing ruminants using nutrition models

This paper was aimed to summarize known concepts needed to comprehend the intricate interface between the ruminant animal and the pasture when predicting animal performance, acknowledge current efforts in the mathematical modeling domain of grazing ruminants, and highlight current thinking and technologies that can guide the development of advanced mathematical modeling tools for grazing ruminants. The scientific knowledge of factors that affect intake of ruminants is broad and rich, and decision-support tools (DST) for modeling energy expenditure and feed intake of grazing animals abound in the literature but the adequate predictability of forage intake is still lacking, remaining a major challenge that has been deceiving at times. Despite the mathematical advancements in translating experimental research of grazing ruminants into DST, numerous shortages have been identified in current models designed to predict intake of forages by grazing ruminants. Many of which are mechanistic models that rely heavily on preceding mathematical constructions that were developed to predict energy and nutrient requirements and feed intake of confined animals. The data collection of grazing (forage selection, grazing behavior, pasture growth/regrowth, pasture quality) and animal (nutrient digestion and absorption, volatile fatty acids production and profile, energy requirement) components remains a critical bottleneck for adequate modeling of forage intake by ruminants. An unresolved question that has impeded DST is how to assess the quantity and quality, ideally simultaneously, of pasture forages given that ruminant animals can be selective. The inadequate assessment of quantity and quality has been a hindrance in assessing energy expenditure of grazing animals for physical activities such as walking, grazing, and forage selection of grazing animals. The advancement of sensors might provide some insights that will likely enhance our understanding and assist in determining key variables that control forage intake and animal activity. Sensors might provide additional insights to improve the quantification of individual animal variation as the sensor data are collected on each subject over time. As a group of scientists, however, despite many obstacles in animal and forage science research, we have thrived, and progress has been made. The scientific community may need to change the angle of which the problem has been attacked, and focus more on holistic approaches.

Benefits and costs of grazing various proportions of perennial ryegrass and chicory for dairy production

Understanding the economic trade-off between changes in the supplementary feed required and the cost of pasture renovation is important when considering investing in alternative forages. Perennial ryegrass (Lolium perenne L.) is the main pasture species used for dairy production in temperate Australia. Alternatives to perennial ryegrass are grown to complement the seasonal growth pattern of perennial ryegrass, and to potentially increase annual dry matter (DM) yield. A case study analysis of a dairy farm in Gippsland was used to explore the benefits and costs over 15 years when either 0%, 20% or 40% of the milking area was sown to chicory (Cichorium intybus L.), with the balance sown to perennial ryegrass. Chicory was part of a 3-year pasture renovation cycle; in the year of establishment, annual ryegrass was sown in the autumn, with chicory sown in spring, followed by 27 months of production. This was compared with a 5-year renovation cycle of perennial ryegrass. Stocking rates of 3.3 and 2.5 cows/ha were modelled. A whole farm budget approach with stochastic simulation was used to quantify the potential effect on profit and risk. The profitability of growing chicory depended on the balance among (1) savings in supplementary feed costs during summer and autumn, and (2) possible reductions in the overall supply of DM during winter and early spring, and (3) increased pasture renovation costs. Stocking rate influenced the most profitable percentage of land sown to chicory. When stocking rate was 3.3 cows/ha, sowing 20% of the milking area to chicory returned a net present value (NPV) over 15 years AU$31 000 greater, on average, than did sowing 0% chicory, and AU$46 000 greater than sowing 40% chicory. With 2.5 cows/ha, sowing 40% of the milking area to chicory returned an NPV AU$39 000–AU$102 000 greater, on average, than did sowing either 20% or 0% chicory, respectively. The ratio of perennial ryegrass to chicory had little effect on the variability of NPV. For an individual farm, the most profitable percentage will fluctuate over time with variations in prices, seasonal conditions and management choices.

Evaluating the economics of concentrate feeding decisions in grazing dairy cows

Purchased concentrates are a significant variable cost of a dairy business. Farm economic theory states that feeding supplements will enable a dairy farmer to improve profit as long as the marginal revenue received from the milk produced exceeds the marginal cost of the supplement. To do this, the quantities of milk, milk protein and milk fat produced from a unit of concentrate added to the diet are needed. Recent research has compiled results from short-term concentrate feeding experiments conducted in Victoria over a 30-year period. Using these data, relationships for the response of milk production to cereal grain supplements in dairy cows grazing temperate pastures have been developed and shown to be a better predictor than previous relationships. These response functions were used in the present study to investigate the economics of tactical (short-term; weekly, monthly or seasonally) and strategic (medium- to longer-term) supplementary feeding decisions in a pasture-based system, including, specifically, how much concentrate should be fed in a particular farm situation, given a certain feed cost and milk price. In the present paper, the relevant production economics method is explained and applied to determine the amount of supplement to feed that will maximise the margin of total extra milk income minus the total cost of supplement, thereby adding the most to farm profit. Currently, when dairy farmers make decisions about how much more supplement to feed their herd, they are making implicit judgements about the extra milk, and other potential benefits, that they expect to result as well as what the milk will be worth. More finely tuned decisions about feeding supplements based on comparing marginal cost and marginal revenue would add more to farm profit than decisions based on other common criteria, such as feeding supplement for maximum milk production. While some farmers may already be feeding supplements close to the point where marginal cost equals marginal revenue, the formal method of marginal analysis reported here makes explicit what is done implicitly at present and tests farmers’ intuitive decision-making. More detailed information about the responses to supplements and the costs and benefits of feeding supplements under particular circumstances at different times through the lactation has the potential to enable better, more profitable decisions to be made about feeding cows and managing the whole farm.

Invited review: Practical feeding management recommendations to mitigate the risk of subacute ruminal acidosis in dairy cattle

Rumen health is of vital importance in ensuring healthy and efficient dairy cattle production. Current feeding programs for cattle recommend concentrate-rich diets to meet the high nutritional needs of cows during lactation and enhance cost-efficiency. These diets, however, can impair rumen health. The term "subacute ruminal acidosis" (SARA) is often used as a synonym for poor rumen health. In this review, we first describe the physiological demands of cattle for dietary physically effective fiber. We also provide background information on the importance of enhancing salivary secretions and short-chain fatty acid absorption across the stratified squamous epithelium of the rumen; thus, preventing the disruption of the ruminal acid-base balance, a process that paves the way for acidification of the rumen. On-farm evaluation of dietary fiber adequacy is challenging for both nutritionists and veterinarians; therefore, this review provides practical recommendations on how to evaluate the physical effectiveness of the diet based on differences in particle size distribution, fiber content, and the type of concentrate fed, both when the latter is part of total mixed ration and when it is supplemented in partial mixed rations. Besides considering the absolute amount of physically effective fiber and starch types in the diet, we highlight the role of several feeding management factors that affect rumen health and should be considered to control and mitigate SARA. Most importantly, transitional feeding to ensure gradual adaptation of the ruminal epithelium and microbiota; monitoring and careful management of particle size distribution; controlling feed sorting, meal size, and meal frequency; and paying special attention to primiparous cows are some of the feeding management tools that can help in sustaining rumen health in high-producing dairy herds. Supplementation of feed additives including yeast products, phytogenic compounds, and buffers may help attenuate SARA, especially during stress periods when the risk of a deficiency of physically effective fiber in the diet is high, such as during early lactation. However, the usage of feed additives cannot fully compensate for suboptimal feeding management.

Comparing the profitability of a dairy business with alternative investments

In the present study, the profitability of a dairy-farm case study evaluated over the period 2003–2004 to 2014–2015 was compared with the performance of other dairy farms and other non-agricultural investments over the same time. Investments are generally made on the expectation that a net return will be earned that justifies using capital in one particular way rather than an alternative way. The expected, and actual, returns from capital invested in different assets will differ according to the risks involved. Investors choose an investment, and mixes of investments, that align with their goals, preferences for risk and anticipated returns over time. Dairy farming involves investing in assets, such as land and improvements, water, livestock, plant and equipment, and people, which are managed to produce milk and ultimately to earn a competitive return on capital. With uncertain seasonal conditions, fluctuating costs and prices, declining terms of trade, wide ranges of equity and management abilities, and a steady decline in the number of commercial farm businesses, it may be tempting to presume that investing in farming, and dairy farming in particular, is a hard road, leading to lower and more variable returns than investing in non-agricultural investment opportunities in the economy. This need not be the case. Analysis of how a dairy business in northern Victoria performed from 2003–2004 to 2014–2015 showed that this farm did well compared with (i) other dairy businesses in Victoria and (ii) alternative investments, such as shares, bonds and property, over the same time. Compound annual return to capital for the dairy farm over the 12 years studied was 12.4% (real, before tax). Over half the return came from the farming operations and the remainder came from owning assets that appreciated in value, particularly in this case, water. The dairy business that was studied was well managed and earned higher annual average returns than the average returns of investments with similar risk elsewhere in the economy, such as shares, and matched it with the best performing of these alternative investments.

Is systems research addressing the current and future needs of dairy farms?

During the past decade, Australian and New Zealand dairy farmers have been increasingly exposed to volatility in milk prices, declining terms of trade, climate variability, changing regulation, and increasing consumer demand to demonstrate their ‘social licence to farm’. In response to the varying challenges, it is not surprising that we see significant diversity in dairy-farm systems in Australia and New Zealand. Despite much research effort to address these challenges at both the component and farm-system level, the evidence of adoption and dairy farming-system change over the past 5 years has been inconclusive. The present review explores how farmers and systems research have been affected and are responding, and whether systems research is developing research in the appropriate direction, proactively researching dairy-farming systems that are resilient, profitable and sustainable into the future, notwithstanding the increased volatility that dairy farms are experiencing. While much farm systems research in Australia and New Zealand has addressed the challenges associated with improving productivity and profitability, and the known challenges such as climate variability and improving environmental outcomes, there is need to fore-sight future risk, challenges and opportunities for dairy systems. It is also important that the system researchers explore alternative approaches such as working collaboratively with the known system experts, the dairy farmer, in a participatory environment to increase rate of knowledge transfer and adoption of positive research outcome.

Pasture and the theory of diversification

Diversifying farm activities can reduce the business risk of agricultural production. The aim of the present study was to investigate the effect of diversifying the types of dairy pastures sown on (1) the average seasonal growth rate (kg DM/ha/day) of pasture and (2) the variability of seasonal growth rate of pasture over time by diversifying the types of pastures grown on a dairy farm. This approach is similar to the approach used to assess the diversification of annual cropping activities, although repeated harvest of pasture by grazing animals and the seasonality of pasture DM production complicates the question. The question investigated was ‘How does substituting chicory (Cichorium intybus L.) or tall fescue (Festuca arundinaceae Schreb.) monocultures for a perennial ryegrass (Lolium perenne L.)–white clover (Trifolium repens L.) pasture in increasing proportions affect (1) the average growth rate (kg DM/ha.day) of pasture and (2) the variability of growth rate of pasture in each season?’. The biophysical model DairyMod was used to simulate 30 years growth of a mixed sward of perennial ryegrass and white clover and monocultures of chicory and tall fescue for two rain-fed locations in the high-rainfall zone of southern Australia. Including chicory in the pasture base had the potential to increase pasture growth rate during the summer–early autumn period compared with growing perennial ryegrass–white clover alone. This increase in pasture growth rate increased variability, and reduced growth rates in late autumn–winter and spring. The simulated growth rates of tall fescue and perennial ryegrass were strongly correlated in all seasons; hence, tall fescue did not reduce the variability of total DM. Further analysis would include price correlations and variability and consider the whole-farm implications. The analysis presented here for the high-rainfall zone showed that introducing alternative forages may have benefits in terms of increasing pasture growth rates at critical times of the production year, but the variability of the growth rate was not reduced.

Supplementary feeding options to alleviate the impacts of decreased water availability on dairy-farm economic performance in northern Victoria

The anticipated effects of climate change, competing demands from the environment, industry and urban users, and changes in water policy are likely to reduce the amount and increase the variability of water allocations to dairy farmers in northern Victoria. The way two irrigated dairy farms that differed in feedbase characteristics, herd size and farm area, would operate and perform with reduced and more variable water allocations was examined over 10 years. Strategies to manage the impact of changed water availability were tested; namely, increasing milk production by feeding more supplementary feed, changing the feed system to present supplements in a partial mixed ration (PMR), and increasing milk production by using a PMR. Neither farm was profitable under medium climate change, or if the conditions that generated the low inflows of water into irrigation supply dams between 1996–97 and 2006–07 prevailed, unless changes were made to the farm system. Feeding supplements in a well formulated mixed ration have the potential to increase the efficiency of metabolisable energy use and offers the opportunity to increase feed intake and milk production. A PMR system enabled one of the farms to maintain and increase profit under medium climate change conditions; however, risk, measured as variability in profit, also increased. Under more severe reductions in water availability, neither of the farms examined was profitable over the run of years. Changes to the farm system other than feeding additional supplementary feed to increase milk production and/or using a PMR system, would be needed to counteract the effects of reduced and more variable water availability and maintain profit.

Use of partial mixed rations in pasture-based dairying in temperate regions of Australia

There is a growing diversity and complexity of dairy farming systems in Australia. Feeding systems based on the provision of mixed rations to dairy cows grazing perennial pastures (termed partial mixed rations or PMR systems) have emerged and present the dairy industry with opportunities for improved production and feed efficiency, but also with significant challenges. Early research results are beginning to define the situations in which PMR systems are profitable and the mechanisms responsible for the improved milk responses. This review focuses on the role of PMR feeding systems in temperate dairying regions of Australia, highlights initial research findings, and identifies some of the gaps in current knowledge that warrant further research. The key findings were that, when very low allowances of pasture are offered to cows, milk production responses were driven mostly by increases in dry matter (DM) intake, and there appeared to be a minimal contribution to increased energy supply from improved whole tract DM digestibility. Differences in milk responses became apparent when >10 kg of total supplement DM was consumed (0.75 : 0.25 concentrate to forage) as PMR. There was a consistent maintenance of milk fat concentration when increasing amounts of concentrates were consumed as PMR, in contrast with supplements consumed in the dairy. There was also a consistent finding that replacing some wheat in the PMR with canola meal resulted in cows consuming more grazed pasture despite the limitations of very low pasture allowances (10–15 kg DM/cow.day, expressed to ground level). This was accompanied by further increases in energy-corrected milk yield. The potential to improve DM intake was further highlighted when pasture allowance was increased, with intake increasing from 3.6% to 4.5% of liveweight (from 20 to 25 kg DM/day for a 550-kg cow). There was also an indication that ~50% of the milk production benefit from PMR can be captured by providing the concentrate supplement as a grain mix in the dairy. There did not appear to be negative impacts of PMR systems on the social and grazing behaviour or health of cows.